Gene expression profiling from ffpe samples

ABSTRACT

Methods and compositions relating to the generation and use of gene expression data from tissue samples that have been fixed and embedded are provided. The data can electronically stored and implemented as well as used to augment diagnosis and treatment of diseases.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application claims benefit of priority from U.S. ProvisionalApplication 60/418,103 filed 11 Oct. 2002, which is hereby incorporatedin its entirety as if fully set forth.

TECHNICAL FIELD

The present invention relates to the amplification of expressed nucleicacid molecules in samples that have been fixed by formalin, formaldehydeor paraformaldehyde. The samples may be those embedded in wax and/orstored for extended periods of time.

The invention also relates to the use of the amplified nucleic acidmolecules to determine gene expression levels in said samples and thecorrelation thereof to various diseases and conditions. The informationon gene expression levels may be electronically stored and used toassist in the diagnosis and treatment of disease.

BACKGROUND ART

Gene expression analyses of various tumor types (breast, lung, prostateand colon) have revealed that there exist numerous subtypes of tumorswithin each anatomically defined cancer. Furthermore, in some of thesestudies different subtypes have been linked to a particular prognosis.For example, Wigle et al, (1) and Beer et al., (2) demonstrate theexistence of particular clusters of genes that are correlated withdifferent disease-free survivals in non-small cell lung cancer. Thesereports establish that the molecular “make-up” of tumors, as defined bygene expression profiles, has a direct correlation to clinical endpointssuch as disease free survival. These retrospective studies stronglysuggest that in going forward with prospective trials there is greatpromise that the molecular make-up of a given tumor will be directlycorrelated with whether a patient will respond or not respond to a giventherapy.

One means of conducting retrospective studies is by use of clinicalsamples, which are of two major types: frozen samples and those thathave been formalin fixed and paraffin embedded. There are, however, atleast three major factors to take into consideration when completing agene expression analysis of clinical samples. First, the use of frozensamples for microarray experiments requires a large amount of tissue andin the current experimental design and methods used by mostinvestigators, a single microarray experiment will “use up” the entirebiopsied material thus significantly restricting the use of the materialfor post-microarray validation experiments, other microarrays withdifferent content, or other types of studies (such as proteomicanalyses).

Second, microarray studies to date generally start with a homogenizedbiopsy and thus have to work with only samples that are highly enrichedfor tumor in order to minimize the amount of cellular heterogeneitywithin the sample. Unfortunately, this is not the “real world” situationin a clinical trial, where there is an inability to choose which subsetof biopsies will be subsequently examined. The use of laser capturemicrodissection (Emmert-Buck et al., 3) obviates this issue by enablingthe selection and capture of the desired cell type regardless of tumorload. “Real world” samples include those where the tumor load may beextremely low (i.e., 10%), and thus the sample may be heterogeneous withrespect to total number of different cell types present in the biopsy,or the sample may contain a large amount of infiltrating inflammatorycells.

Finally, routine processing of samples in the clinical setting issignificantly different from that conducted in a research laboratory. Inparticular, for routine analysis of biopsies from a clinical setting,the tissue is processed by formalin fixation and subsequently paraffinembedded. This process is a highly efficient method that is currentlythe standard in pathology suites. Unfortunately, only frozen samples arebeing currently utilized for microarray analyses because of the generaltechnical inability of obtaining mRNA from formalin fixed samples forglobal mRNA expression analysis (i.e. for hybridization to cDNA or oligomicroarrays). For example, Lewis et al. (5) expressly state that loss ofpoly A tails from mRNA is “the main cause of failure of the reversetranscription step”.

Other attempts to utilize formalin-fixed tissue to produce cDNA forsubsequent experiments have generated mixed results. For example,Karsten et al., (4) compared the use of frozen versus formalin-fixedtissues for use in cDNA microarrays via a tyramide signal amplification(TSA) system and concluded that “ . . . formalin-derived RNA was not agood substrate for cDNA synthesis and clearly did not produce reliablehybridizations in our microarray experiments”. On the other hand, Cohenet al. (9) describe the use of reverse transcription using randomhexamers and real-time quantitative RT-PCR to amplify and thus detectexpression of two chemokines. Similar use of reverse transcription PCRto amplify and detect expression of individual gene sequences wasdescribed by Lewis et al. (5), Lehmann et al. (6), Specht et al. (8),Masuda et al. (10), and Danenberg et al.(11). There has been no reportedmeans to analyze gene expression at a cellular level by globalamplification of extracted nucleic acids and subsequent analysis bymultiplex analysis such as by use of a microarray.

Citation of documents herein is not intended as an admission that any ispertinent prior art. All statements as to the date or representation asto the contents of documents is based on the information available tothe applicant and does not constitute any admission as to thecorrectness of the dates or contents of the documents.

DISCLOSURE OF THE INVENTION

The present invention provides a means to analyze the expression ofvarious nucleic acid sequences in cells that have been fixed andoptionally embedded. The act of fixation may be viewed as “freezing” thelevel of expression to that present in the cells at the time offixation. The expression levels of various sequences, particularly asmRNA molecules in the cells, may thus be considered as having beenfrozen in time. A dynamic scene of cellular gene expression is thuscaptured as static molecules which represent the expression levels ofvarious gene sequences in time. The invention provides a means ofquantifying those expression levels, or viewing that scene, by thesimultaneous generation of a plurality of cDNA molecules from the mRNApopulation of a cell. This “global” analysis of mRNA expression may befollowed by subsequent transcription of said cDNA to produce RNAmolecules for assay.

By rough analogy to a traditional photographic process, the expressionlevel “scene” captured by fixation is used to generate cDNA “negatives”from which amplified RNA molecules may be produced for assay, such asone based on an array (or array-able) format such as a microarray. Thearray, which can contain a plurality of sequences capable of hybridizingto the amplified RNA molecules, is thus a “photograph” depicting geneexpression in a cell.

The invention thus provides a means to “unlock” the gene expression datain a fixed and embedded tissue sample (or view the expression levels inthe cells in such a sample) by the use of techniques to prepare andanalyze the levels of messenger RNA molecules in said cells. Inpreferred embodiments, the invention is used quantitatively to determinethe level of expression of one or more nucleic acid sequences.Alternatively, the invention may be used qualitatively.

Generally, a fixed cell containing tissue sample serves as the source ofcell containing material for the practice of the invention. The sampleis preferably sectioned and used for the extraction and preparation ofRNA, optionally preceded by microdissection and/or removal of theembedding material. The extracted RNA is optionally heated totheoretically de-modified and restore the RNA to a more native,pre-fixative, state. Polyadenylated RNA is then amplified by initiallyconverting it, without selection, to cDNA via the use of an oligo dTprimer which preferably is operatively linked to a promoter sequencethat can direct transcription of the cDNA. The promoter may be a singlestranded sequence (which is converted to a double stranded sequence uponsynthesis of the second cDNA strand) or double stranded. This may befollowed by transcription of the cDNA to produce amplified RNA havingthe same, or complementary sequence of the extracted RNA material. Theamplified RNA is “global” because it is based upon polyadenylationrather than on selection of any particular gene sequence(s).Nevertheless, the RNA may be used to determine, or analyze for,sequences corresponding to the expression of nucleic acids in the cell,such as by hybridization to sequences on an array (or sortable array)format such as a microarray. Alternatively, the cDNA may be analyzed byother methods, including direct amplification (such as, but not limitedto, PCR as discussed further below).

In an initial aspect, the invention provides an initial extraction andpreparation of RNA from fixed cells method using a combination ofproteinase treatment followed by RNA extraction and contact with asilica matrix. The extraction is preferably performed by use of aguanidinium containing compound or other means of producing thechaotropic effects of such compounds to denature proteins. This improvesthe condition of the RNA for subsequent analysis.

In a second aspect, the invention provides an improved method ofpreparing the RNA for reverse transcription by heating it. Without beingbound by theory, this is believed to result in de-modification of RNAbases which were modified during fixation of the cells. This improvesthe condition of the RNA for subsequent uses.

In a third aspect, the invention provides an amplification method basedupon amplifying RNA molecules containing poly A sequences at the 3′ end.Such molecules have previously been determined to be degraded beyond theability to serve as templates for reverse transcription (5). Theamplification is made possible by initially reverse transcribingtemplate polyadenylated RNA with an oligo dT primer, optionallycomprising an operatively linked single or double stranded sequence of apromoter sequence. Reverse transcription of polyadenylated RNA ingeneral permits the simultaneous production of a plurality of cDNAmolecules which reflect the levels of the template polyadenylated RNAmolecules of the cell. The invention may also be applied to theamplification of polyadenylated RNA molecules expressed by a pathogen aspresent in a fixed tissue sample.

In particularly preferred embodiments of the invention, all three ofthese aspects of the invention are combined for use together to produceinformation concerning gene expression in a fixed tissue sample.

The cDNA molecules may be used to transcribe RNA molecules containingthe sequences of the template polyadenylated RNA or to transcribe RNAmolecules complementary to such sequences. These transcribed moleculesmay be optionally labeled and used for hybridization to complementarysequences, such as those present on a microarray, to detect andoptionally quantify, the expression of various sequences in the cell(s)from which the template polyadenylated RNA was isolated. Alternatively,the transcribed molecules are used to produce labeled cDNA molecules forhybridization to an array. The cDNA prepared from the templatepolyadenylated RNA, subsequent amplified mRNA, and optional subsequentcDNA, all optionally hybridized on a microarray, are products of theinvention.

The cDNA molecules prepared from the template polyadenylated RNA mayalso be used in other methods of nucleic acid analysis. Non-limitingexamples include PCR and quantitative or real time PCR amplification todetermine, or analyze for, the expression levels of particular sequencesvia the use of specific primers. While the amplification may beperformed in combination with hybridization to a microarray, thisapproach is not “global” because the PCR process requires the use ofparticular sequences in one or more primers which selectively amplifysome sequences for analysis. These methods may be used to determine theexpression levels of particular gene sequence(s) identified ascorrelated with an outcome as described below.

In another aspect, the invention is utilized in combination with fixedsamples of tissue from subjects, preferably human, afflicted with, orsuspected of having, a disease or other unwanted condition. Samples fromsubjects having the same disease or unwanted condition are preferablyused in combination to identify the expression levels of genesequence(s) as correlated with one or more aspects of the disease, ortreatment or outcome thereof. Such samples have been collected over timeand are often associated with detailed information on the disease,condition, treatment and/or outcomes of the subjects after the samplewas taken. Non-limiting examples of such information includes thatrelating to the diagnosis, prognosis, treatment, response to treatment,and/or actual outcome(s) experienced by the subject over time aftercollection of the sample for fixation. In an alternative aspect, theexpression levels of gene sequence(s) may be correlated with thecondition of the subject prior to tissue sampling. Non-limiting examplesinclude pre-existing diseases or unwanted conditions, age of diseaseonset, infection by infectious agents, exposure to mutagens or toxicagents, or genetic disorders. Such correlations are retrospective innature, as opposed to correlations with outcomes that are to occur,which are prospective in nature. Furthermore, the expression levels ofgene sequence(s) may be correlated with information on a disease,condition, treatment and/or outcome of the subject after the sample usedto determine gene expression levels is obtained. The invention may thusbe used to correlate gene expression with retrospective as well asprospective information from a subject from whom the sample wasobtained. The correlations may be used to generate a model to assistclinical diagnostics by application of the correlations between geneexpression level(s) and outcome(s).

In a further aspect, the invention provides for the compilation of theinformation concerning the expression levels of a plurality of nucleicacid sequences in the cell(s) of a fixed sample into a data structure.The data structure is optionally embedded in a solid medium or otherarticle of manufacture, such as, but not limited to, a computer readableor other electronically readable medium. Preferably, the arrangement ofthe data structure permits the ready utilization of the informationconcerning expression levels to be used in methods of interpreting andutilizing expression level information in combination with an aspect ofa disease, or treatment or outcome thereof. Correlations of geneexpression levels with an aspect of a disease, or treatment or outcomethereof, may be stored as part of the same data structure or as aseparate data structure.

The invention also provides for the ability to apply these correlationsto gene expression information from a sample from another subject toidentify said sample has having the same expression levels and thesubject as likely to have the same aspect(s) of a disease, orsusceptible to the same treatment or outcome thereof. Such samples fromanother subject include those that are not fixed, such as, but notlimited to, a fresh or frozen sample. The expression level informationfrom such other samples need not be obtained by the practice of thepresent invention, but rather may be by the use of other means,including, but not limited to, RT-PCR amplification of individual genesequences and detecting expression of protein(s) encoding by theexpressed sequence(s). Such methods of interpreting and utilization areoptionally computer implemented.

The nucleic acid expression information in such a data structurepreferably comprises information from one or more fixed tissue samplesfrom six months to over 100 years ago and preferably comprisesinformation concerning the post fixation treatments and/or outcomes ofthe subject from which the sample was taken. The information from aplurality of samples from a plurality of subjects may be correlated toidentify specific expression levels of one or more gene sequences asrelevant to an aspect of a disease or the post fixation treatmentsand/or outcomes of the subjects. This information may be applied inwhole or in part to form all or part of a clinical definition oridentification of a disease or unwanted condition in a subject. It canalso be used to prognosticate as to the likely outcome experienced byother subjects with the same expression profiles in their tissuesamples. The information may also be applied to use the expressionlevel(s) of one or more sequences as defining a population orsubpopulation of a larger group based upon diagnosis, prognosis,treatment, response to treatment, and/or actual outcome(s) correlatedwith the expression level(s). It may also be used to identify newaspects of a disease or treatment thereof based upon a relationship tothe expression of one or more sequences.

In yet another aspect of the invention, methods of applying orinterrogating this information to identify a cell containing sample fromanother subject as having the same expression level(s), and thusbelonging to a population or subpopulation, are provided. The samplefrom another subject need not be fixed, but may be a fresh or frozensample as non-limiting examples. These methods may be optionallycomputer implemented to maximize the beneficial application of theinformation that correlates expression level(s) to diagnosis, prognosis,treatment, response to treatment, and/or actual outcome(s). Thesemethods would be advantageous in clinical applications of the inventionto assist doctors and other medical personnel with the treatment and/orcounseling of patients.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 shows RNA extracted from tissues fixed in formalin for 1 to 8days.

FIG. 2A shows RNA amplified from tissue samples fixed in formalin for 1,4, or 8 days as well as fresh frozen tissue. FIG. 2B shows additionalresults of tissue samples fixed for 4 days.

FIG. 3A shows RNA amplification from archival FFPE samples of about 1-2years old. FIG. 3B shows the results of RNA amplification from four sixyear old archival FFPE breast core biopsies.

FIG. 4 shows RNA amplification from about 1 to 4 years old bladdercancer FFPE samples.

FIG. 5 shows a scatter-plot of signal intensities from two independenthybridizations of RNA amplified from an FFPE sample.

FIG. 6 shows a scatter-plot of signal intensities from an FFPE versus afrozen sample.

FIG. 7 shows the relative yield of RNA amplification of 3′ sequencesfrom FFPE samples fixed in formalin for various times afterdemodification with heat.

FIG. 8 shows the relative yield of RNA amplification of longer 3′sequences from FFPE samples fixed in formalin for various times afterdemodification with heat.

FIG. 9 shows a comparison of microarray data generated by use ofamplified RNA prepared from cDNA prepared by the use of random primersor in the absence of random primers.

MODES OF CARRYING OUT THE INVENTION

The present invention provides for the global mRNA profiling of cellsfrom (routine) clinical biopsies that are formalin-fixed (FF) andoptionally paraffin-embedded (FFPE). Stated differently, the inventionprovides for the analysis of global mRNA expression in cell(s) of an FFsample. The invention may be applied to determine the expression ofvarious genes within cells of a biopsy as well as serve as an indicatorof protein expression within the cell.

In one embodiment, the invention optionally utilizes a microdissectiontechnique to isolated cells from a formalin-fixed tissue sample followedby an RNA extraction protocol and subsequent amplification of mRNA topermit global mRNA expression profiling. The isolated cells arepreferably those that appear to be non-normal. Normal cells may also beisolated and used as control cells. The identified expression profilemay then be optionally used to identify gene sequences, the expressionof which define a molecular expression signature for the cells and thecondition which they are in. Such conditions include, but are notlimited to, disease conditions, types, states, stages, and/or substagesor subtypes. In preferred embodiments, the signature(s) (or expressionlevels) are used with historical data concerning the subjects from whichthe tissue samples were obtained to identify the cell(s), and thus asubject containing such cell(s), as sensitive or resistant to varioustreatment protocols. This information may then be used to directtreatment (to utilize the more effective treatment) in another subject,or a human patient, identified as having cell(s) with the samesignature(s). In other embodiments, the expression levels are used withprospective data from the subject from which a sample was obtained.

In a particular exemplification of the invention, a process forobtaining gene expression data from FFPE samples is provided wherein theprocess comprises:

-   -   (1) Isolating a cell containing portion the FFPE sample, for        example by microdissection (such as, but not limited to, laser        microdissection),    -   (2) Extracting the sample to collect an mRNA containing        fraction,    -   (3) Optionally purifying the mRNA,    -   (4) Amplifying the mRNA, optionally using a method comprising:        -   a. First strand DNA synthesis by reverse transcription with            a primer containing both a poly (or oligo) dT region and a            promoter portion,        -   b. Second strand synthesis using exogenously supplied,            random primers,        -   c. In-vitro transcription (IVT) originating from the            promoter present in said primer (optionally made double            stranded via said second strand synthesis) to generate            multiple copies of RNA molecules containing sequences            complementary to the mRNA in the FFPE sample, and    -   (5) Analysis of gene expression (as represented by mRNA levels)        in the sample via hybridization of the IVT transcribed RNA to a        microarray containing sequences of various gene sequences.

The invention may be practiced with samples fixed and embedded with avariety of methods known in the art. Briefly, such methods usually beginwith cell containing tissue obtained from a patient afflicted with, orsuspected of having, a disease or other unwanted condition. Non-limitingexamples of tissue samples include a core biopsy, a removed tumortissue, and a cytology sample. Other non-limiting examples include fineneedle aspirates (FNA), needle biopsies, and ductal lavage samples.Non-limiting examples of tissue type include pancreas, large intestine,cancer of large intestine, muscle, urinary bladder, kidney, lung, brain,lymphoma, and any other tissue of a multicellular organism.

The sample is quickly immersed in a fixative means such as a solutionwith a protein crosslinking activity, such as but not limited to aformaldehyde solution, glutaraldehyde solution, formaldehyde-alcoholmixed solution, alcohol solution, Bouin's solution, Zenker solution,Hely solution, osmic acid solution, Carnoy solution, and equivalentsthereof. Non-limiting examples of fixative alcohols include ethanol andisopropanol. This is preferably done as quickly as possible to minimizecellular changes that may occur after collection and before fixation. Italso maintains the fine structure of the tissue and cells therein.

The fixative preferably contains formaldehyde or paraformaldehyde orother means of fixing tissue samples. Preferred fixatives includebuffered formaldehyde, such as phosphate-buffered formaldehydesolutions, or other means of buffering formaldehyde or paraformaldehyde.The fixed samples may be maintained as “wet samples” considered as partof a “wet archive” or are optionally treated with an embedding meanssuch as paraffin or other wax like hydrocarbons. While other fixativessuch as acetone, Clark's, Carnoy's, glutaraldehyde, mercuric chloridecontaining formaldehyde formulations, and Bouin's fixative may be used,the invention is preferably practiced with the large number of archivaltissue samples that are formalin fixed and paraffin embedded (FFPE). Thefixatives may optionally contain magnesium cations.

The time of fixation is preferably from 16 to 48 or 72 hours attemperatures from about 4° C. to room temperature. Times of about 16,about 20, about 24, about 28, about 32, about 36, about 40, about 44,about 48, about 52, about 56, about 60, about 64, about 68 and about 72hours may be used in the practice of the invention. Alternatively,shorter times of about 3, about 4, about 5, about 7, about 8, about 9,about 10, about 12, about 14, and about 15 hours may also be used. Suchshorter periods may be more appropriate for smaller samples, such as inthe case of FNA or needle biopsy samples. Temperatures of about 4, about8, about 12, about 16, about 20, about 24 and about 26° C. may be usedThe invention may also be practiced with a sample fixed for other times,such as for 4, 5, 6, 7, or 8 days and at other temperatures than thosedisclosed herein. After fixation, the samples may be embedded inparaffin using standard techniques and means for embedding followed bystorage under art utilized conditions, such as at temperatures fromabout 4° C. to room temperature.

The age of the fixed and embedded samples are preferably from about 6months to about 100 years old for the practice of the invention tocorrelate expression levels with actual outcomes of the patient fromwhich the samples were taken. Obviously, samples less than about 6months of age may also be used in the practice of the invention, but itmay not be possible to correlate the expression levels in such sampleswith actual outcomes of the patient from which they were obtained due tothe short time interval. The expression levels of samples withoutassociated outcome information may nonetheless be used in comparison tothe expression levels and correlated outcomes generated by the use ofthe invention with older samples.

Preferred older samples for correlation of expression levels to actualoutcomes are about 6 months, about 1 year, about 2 years, about 3 years,about 4 years, about 5 years, about 6 years, about 7 years, about 8years, about 9 years, about 10 years, about 11 years, about 12 years,about 13 years, about 14 years, about 15 years, about 16 years, about 17years, about 18 years, about 19 years, about 20 years, about 25 years,about 30 years, about 40 years, about 50 years, about 60 years, about 70years, about 75 years, about 80 years, about 90 years, or about 100years old.

A section of a fixed sample is preferably used in the present inventionto preserve material of the fixed sample for subsequent uses. Sectioningmay also be used in combination with the optional use of microdissectionas discussed below. Preparation of sections may be by any techniques andmeans for sectioning. In one embodiment, the paraffin blocks are slicedinto sections by the use of a microtome. Preferably, the microtome hasbeen carefully cleaned to remove or reduce the likelihood ofcontamination by extraneous nucleic acid molecules or nucleic aciddegrading agents. A non-limiting example includes the use of anonhazardous zylol substitute along with the use of a 3% hypochloritesolution for the treatment of plastic ware used in combination with thesectioning process.

Sections are optionally, but preferably, deparaffinized by proceduresknown in the art to remove the bulk of paraffin from a sample. Varioustechniques for deparaffinization are known and any suitable techniquemay be used in practicing the present invention. Such methods include,but arc not limited to, washing with an organic solvent or agent todissolve the paraffin. Non-limiting examples of suitable solventsinclude benzene, toluene, ethylbenzene, xylenes, D-limonene, octane, andmixtures thereof. These solvents are preferably of high purity, usuallygreater than 99%.

Paraffin is removed by washing with an organic solvent or agent followedby its removal. The volume of organic solvent used and the number ofwashes necessary will depend on the size of the sample and the amount ofparaffin to be removed. A sample may be washed between 1 and about 10times, or between about two and about four times. A typical volume oforganic solvent is about 500 μL for a 10 μm tissue sample. Other methodsfor deparaffinization may also be used.

After deparaffinization, samples are preferably rehydrated, such as bystep-wise washing with aqueous lower alcoholic solutions of decreasingconcentration. Ethanol is a preferred lower alcohol for rehydrationwhile other alcohols may also be used. Non-limiting examples includemethanol, isopropanol and other C1-C5 alcohols. The sample isalternatively vigorously mixed with alcoholic solutions followed by itsremoval. In one embodiment, the concentration of alcohol is stepwiselowered from about 100% to about 70% in water over about 3 to 5 stepswith an about 10% or less decrease in each step, such as via 100%, 95%,90%, 80%, 70% steps. Deparaffinization and rehydration may also beconducted using other reagents known in the art.

With or without deparaffinization, the sections are optionally stainedto visualize cells within the sections, preferably by use of means thatdo not cause the loss of RNA. Staining with hematoxylin and eosin (H &E) may be in some embodiments of the invention, especially where thereis subsequent use of the optional microdissection step to isolate one ormore individual cells. Staining also permits the evaluation of thesections to determine whether subsequent microdissection is necessarybased upon the presence or absence of contaminating cells which arepreferably not used for the extraction of RNA. The presence of excessinfiltrating immune cells in a sample of cancer cells where geneexpression in the cancer cells is of greatest interest is a non-limitingexample of a situation where microdissection to isolate the cancer cellsfor use is desirable.

Microdissection of a tissue section may be performed by any meanssuitable therefor. Non-limiting examples include laser capturemicrodissection (LCM) or laser microdissection (LMD). The isolation ofcells advantageously permits the exclusion of unrelated cell types suchas, but not limited to, infiltrating immune cells, as well as exclusionof cells of other origins and/or phenotype(s). Microdissection may beadvantageously used in the practice of the invention becausecontaminating, non-disease related cells (such as infiltratinglymphocytes or other immune system cells) may be eliminated from a fixedand embedded tissue sample or section to avoid affecting thedetermination of gene expression in the cells of interest. Anon-limiting example of such contamination is present where a biopsy isfixed and then used to prepare the section. The capture of about100-1000 or more cells is preferred for the practice of the invention,however, the use of fewer cells is also possible.

Microdissected samples that have not been deparaffinized may optionallyundergo paraffin removal by use of the methods described above.

As noted herein, sectioning and microdissection are both optional stepsbefore the extraction of RNA from cells as utilized in the presentinvention. The invention may be practiced with a variety of extractionprotocols, including acid guanidinium thiocyanate/phenol-chloroform,proteinase K digestion at various temperatures and for various times,oligo dT based chromatography, and a guanidinium thiocyanate lysisfollowed by binding to glass beads or another silica based matrix (seereferences 13-15). The present invention also provides, however, a newmethod of RNA extraction as described below. This method has beenunexpectedly found to provide an enhancement in the amount and quantityof RNA extracted from a fixed sample.

The invention also provides for an optional heating step believed tode-modify nucleic acid bases that are often modified due to fixationwith formaldehyde. The invention is not, however, to be bound by thistheory, which is provided to assist with the understanding of theinvention and not as a limitation thereof. The theoretical modificationsare the addition of mono-methylol (—CH₂OH) groups at various rates. Themodified bases have altered basepairing capabilities and so can havedeleterious effects on any aspect of the invention wherein RNA moleculesin the sample are to be hybridized to other nucleic acids, such asduring priming and nucleic acid polymerization events such as reversetranscription.

In particular, the present invention provides for the use of a longerheating period without deleterious degradation of RNA molecules.Preferably, the heating is at 70 or about 70° C. for a period of atleast one hour, preferably greater than 60 minutes, such as 120 or 180minutes although periods up to 8 hours may also be used. The heatingperiod may thus be from greater than 60 to about 75, about 90, about105, about 120, about 135, about 150, about 165, about 180 minutes,about 4 hours, about 5 hours, about 6 hours, about 7 hours, or about 8hours. Most preferred is the use of heat for about 3 hours, such as from150 to 210 or 165 to 195 minutes. And may be performed in a variety ofbuffered solutions, such as, but not limited to, 10 mM Tris-HCl at pH8.0 or thereabouts. Equivalent acetate buffers may also be used. Theability to utilize such conditions is an unexpected discovery in lightof evidence that RNA degradation and decreased yields occur upon 60minutes of heating at 70° C. (see Masuda et al. (6)).

The invention provides a means to globally amplify polyadenylated RNAfrom the cell(s) of a fixed sample by use of a poly or oligo dT primer.The primer is used to hybridize to the poly A tails of mRNA moleculesfor the synthesis of a first cDNA strand. Such strands may be relativelyshort, on the order of about 100-400 basepairs or may be longer, such asup to 1-6 kilobase. This reflects a surprising result based upon theunderstanding in the art that the poly A tails of mRNA extracted fromfixed samples were too degraded to permit reverse transcription via apoly or oligo dT primer (see Lewis et al. (5)). A variety of dT basedpriming methods may be used in the present invention, and non-limitingexamples include those described in U.S. Pat. Nos. 5,545,522, 5,716,785and 5,891,636, where synthesis of a second cDNA strand is performedwithout exogenous primers. A preferred method is described in publishedInternational Application WO 02/052031 (corresponding to PCT/US01/50340filed Dec. 21, 2001) and utilizes random primers for the synthesis ofthe second cDNA strand.

The cDNA may be used for direct analysis of gene expression, such as,but not limited to, being hybridized to labeled polynucleotide probes orbeing labeled for detection followed by hybridization to probes. Or thecDNA may be analyzed indirectly after amplification by a PCR techniquefollowed by detection. Alternatively, the cDNA may be used for in vitrotranscription (IVT) in the manner described in International ApplicationWO 02/052031. Briefly, the first strand cDNA comprises a single strandedor double stranded form of a promoter sequence introduced via anoperative linkage to the poly or oligo dT primer used to synthesize thefirst cDNA strand. The resultant double stranded cDNA may be transcribedby initiation from said promoter to produce mRNA transcripts. Thesetranscripts would contain sequences complementary to that of thepolyadenylated RNA used to generate the cDNA. A primer linked promoterof the invention is preferably a T7 promoter, but other non-limitingexamples include the T3 and SP6 promoters.

In another alternative IVT embodiment, the promoter sequence may beintroduced via an operative linkage to the random primers used tosynthesize the second cDNA strand. The resultant double stranded cDNAmay be transcribed by initiation from said promoter to produce mRNAtranscripts containing sequences of the polyadenylated RNA used togenerate the cDNA. In either of the above IVT embodiments, thetranscribed (or amplified) RNA may be analyzed directly by hybridizationto labeled polynucleotide probes or labeled for detection followed byhybridization to probes. The transcribed RNA may also be analyzedindirectly after amplification by a PCR technique or by conversion tocDNA which is analyzed as described above. Both of these lattertechniques can of course rely upon the use of primers that arecomplementary to sequences at the ends of the cDNA.

In a particularly preferred embodiment, a portion of the amplified RNAis used to produce labeled cDNA conjugated to a fluorescent dye, such asby use of labeled nucleotides. A second, and compatible, fluorescent dyeis used to label a reference amplified RNA. Equal amounts of bothlabeled cDNAs are hybridized to a microarray of various nucleic acidsequences individually located at discrete locations of the microarray.After hybridization and washes, the microarrays are scanned andquantitated for hybridization signal intensity to each sequence on themicroarray. The fluorescent intensities, after normalization, can beexpressed as ratios of each amplified RNA to the reference amplified RNAto represent gene expression levels of the sequences of each amplifiedRNA. Alternatively, the amplified RNA is labeled as it is produced. Thelabeled amplified RNA is optionally fragmented and hybridized to probes,such as, but not limited to, those immobilized on a microarray. The RNAmay be labeled directly for detection, such as by fluorescently orradioactively labeled nucleotides, or labeled indirectly, such as bybiotinylated nucleotides which are detected with a fluorescently orradioactively labeled streptavidin. Therefore, both DNA and RNAmolecules corresponding to the amplified RNA of the invention may beused as probes. Another form of indirect labeling is by use ofallylamine to conjugate a label, such as a fluorescent dye, to a nucleicacid molecule (see Example 1 below for an exemplification).

Preferably, the sequences on the microarrays are those of the 3′portions of various gene sequences expressed in a cell of an FFPE sampleas analyzed by use of the present invention. As recognized by theskilled person, the 3′ portion is closest to the site of polyadenylationand thus most likely to be reverse transcribed, and thus found in theresulting cDNA, in the practice of the present invention.

Information on the expression levels of various sequences, such as, butnot limited to, the ratios of fluorescent intensities as describedabove, may be stored via an appropriate means as preferred by theskilled person. In preferred embodiments of the invention, theinformation is stored magnetically or electronically, and morepreferably in a form that is computer readable. The expression leveldata may be stored as raw data or as processed data (such as, but notlimited to, normalized, corrected, or in the form of ratios) or ascombinations thereof. Preferably, the processed data is in the form ofraw expression levels that has been converted into an expression valueor expression index for each gene sequence from a sample. In preferredembodiments, the information is stored as a data set and/or a datastructure. One non-limiting example is storage as a table with storedrecords. A tabular storage means may be viewed as data fields whichstore information like a subject identifier (with or without informationon expression levels of various sequences from a subject's FF or FFPEsample) and/or a gene sequence identifier. These identifiers may alsoserve as descriptive names for the respective fields. Preferably, boththe subject identifier and the gene sequence identifier fields aredesignated as primary “keys” used to uniquely identify a record. Atabular information storage means of the invention is preferablyspecific for a disease or unwanted condition and may be stored on acomputer-readable medium. They may also be a data structure to supportspecific manipulation, “look up”, or application functions as providedby the instant invention.

In a particularly preferred embodiment of the invention, the geneexpression level information is combined with other information aboutthe donor from whom the FF or FFPE sample was obtained. Preferably, thesubject is a human patient, and such other information includes, but isnot limited to, that which is normally obtained in relation to medicalor clinical treatment. Non-limiting examples include age, weight,height, medical history as well as health status and/or symptoms ordisease type or status at the time the sample was obtained. A furtherexample is information obtained from a pathologist's review of thesample. The latter items are of relevance with respect to patients thatare afflicted with, or suspected of being afflicted with, a disease orother unwanted condition. This additional information may also be storedusing a tabular storage means as described above or in a separatestorage means.

When available, the other information may also include informationconcerning the patient's diagnosis and care following the isolation ofthe sample. Generally, such information is that which is normallymaintained in a patient's medical history over time to record treatmentsand outcomes (including further development, eradication, or remissionsof a disease) as well as a medical practitioner's notes and/orobservations. Non-limiting examples of the latter include cases ofunusual genetic makeup of the patient, difficulties in determining aclear diagnosis or course of treatment, and/or unusual diseaseprogression in spite of treatment. Other non-limiting examples of suchadditional information include that relating to the diagnosis and/orprognosis of the patient, the treatment(s) applied, the responsivenessof the patient and disease to said treatment(s), the presence or absenceof side effects from said treatment(s), the cause and age of death ofthe subject, and other outcome(s) for said patient and disease. Inparticularly preferred embodiments of the invention, informationregarding the treatment(s) applied and the outcome(s) is combined withinformation concerning gene expression levels.

Preferred information relating to outcomes) is that which is collectedover time, including, but not limited to, information concerning thefurther progression, eradication, or remission of the disease, thesuccess or failure of the treatment(s), and life span of the patientfollowing treatment. This additional information may also be storedusing a tabular storage means as described above or in a separatestorage means. Alternatively, it may be combined with a tabular storagemeans as described above by introduction into a receiver object that isused in combination with the tabular storage means. This combination ispreferably stored in the same medium.

Other information that may be correlated with the expression levels ofgene sequence(s) include that of the subject at the time of tissuesampling. Non-limiting examples include pre-existing diseases such asautoimmune disease, unwanted conditions such as excess inflammation, andinfection by a bacterial, viral, or fungal agent. Additionally, the sametype of information collected about the subject after isolation of thesample may be correlated. Such data is prospective in nature, andincludes that from a clinical trial as a non-limiting example. Theinvention may thus be practiced with the use of data that isretrospective and prospective relative to the time of FF or FFPE sampleisolation. Additionally, the invention may be practiced with data thatis retrospective and prospective relative to the time of RNA extractionand cDNA preparation.

The ability to determine the expression levels of various gene sequencesin an FF or FFPE sample provides a unique means to relate the expressionlevels to information concerning disease or patient outcome(s) over timebecause the FF or FFPE sample can serve as a point in time referencefrom which to correlate the outcome(s). FF or FFPE samples that aresufficiently old to be combined with data concerning disease or patientoutcome(s) over time, are thus an archive which can be tapped tocorrelate gene expression with disease progression and outcome.

The invention “unlocks” the archive by providing access to the globalgene expression data stored therein in contrast to other individual bitsof expression data based upon analyses of individual gene sequences. Theability to simultaneously evaluate a plurality of gene sequenceexpression levels in a single sample allows for the data concerningthese levels to be compiled into a data structure for subsequent use,analysis and manipulation.

Generally, means for the compilation of data are known in the art, butthe invention provides means for the combination of the gene expressiondata from FF or FFPE samples with additional information concerning asubject or patient as described herein. The means and resultingcombinations provided by the instant invention provide in part theability to generate molecular models for disease as well as predictivemodels to assist in diagnosis and treatment of disease. The generationand use of this combined data are described further below.

Methods of applying or interrogating the “profile” of gene expressionlevel(s) correlated with an outcome include the diagnosis of a subjectsuspected of having a disease in whole or in part by comparison of geneexpression in a sample obtained from the subject to one or more profilesgenerated by the present invention. The same or similar gene expressionprofiles indicate the presence of the same disease. The profile may thusbe viewed as part of a definition of a disease or as a tool fordifferential diagnosis to exclude other diseases or unwanted conditionsfrom the diagnosis. The profile may also be considered as defining oneor more characteristics of a subject with the same or similar cellulargene expression profile. These characteristics include the variousoutcomes as described herein as well as characteristics that have yet tobe recognized.

The profile may also be used in methods of determining treatment for asubject by using the diagnosis obtained as described above to determinetreatment. Alternatively, the profile may include an indication of anefficacious treatment based upon the treatment outcomes of subjectswhose samples were used to generate the profile. The same or similarprofile of gene expression level(s) in a sample from a subject seekingor in need of treatment would indicate use of the treatment found to beefficacious for the subjects whose samples were used to generate theprofile.

Profiles of the invention may also be used to provide informationconcerning prognosis or counseling to a subject afflicted with adisease. Information on disease outcomes that have been associated withgene expression level(s) of the invention may be provided to subjectswhose tissue samples have been found to have the same or similar geneexpression level(s).

RNA Extraction

RNA may be extracted from cells of an FFPE sample via protocols usingacid guanidinium thiocyanate/phenol-chloroform, proteinase K digestion,oligo dT based chromatography, and a guanidinium thiocyanate lysisfollowed by binding to a silica based medium. The use of proteinase Kdigestion is normally followed by an extraction step using phenol orphenol-chloroform to remove the degraded proteinaceous material as wellas the proteinase K protein for isolation of the RNA. As obvious tothose skilled in the art, proteinaceous material is separated, via thepresence of the non-aqueous phenolic phase, from nucleic acids,including the RNA, which remains in the aqueous phase.

The present invention provides an improved method of RNA extractioncomprising the use of proteinase K followed by denaturation with aguanidinium containing compound as a chaotropic agent to denature thecontaminating proteinaceous material. The RNA is then isolated bybinding to a silica based matrix which does not bind the contaminatingproteinaceous material. This is based in part on the unexpecteddiscovery that a guanidinium containing compound is capable ofdenaturing proteinase K and allowing purification of RNA away from it.The bound RNA may then be eluted from the silica based matrix usingconventional means for subsequent manipulations.

Non-limiting examples of guanidinium containing compounds includeguanidinium isothiocyanate (GITC or guanidinium thiocyanate, GSCN) andguanidinium hydrochloride. They may be used with a variety of anioniccounterions from which appropriate ones may be selected by the skilledpractitioner. The guanidinium solution used in the invention generallyhas a concentration in the range of about 1 to about 5M with a preferredvalue of about 4M and is preferably buffered to a pH of about 3 to about6, more preferably about 4, with a suitable biochemical buffer such asTris-HCl. The guanidinium containing solution may optionally contain oneor more RNAse inhibitors.

Other chaotropic agents with the activity of guanidinium containingcompounds may also be used as long as an effective concentration RNA ispurified from an FFPE sample in an amount equivalent to that using aguanidinium containing compound. Non-limiting examples of such agentsinclude urea, formamide, potassium iodide, potassium thiocyanate andequivalents thereof.

The proteinase K treatment is preferably performed at a temperature of42° C. or thereabouts to 60° C. for at least 8 hours, preferably atleast 16 hours, and more preferably at least 24 hours. Other conditionsmay be any that are suitable for RNA extraction. A non-limiting exampleis 10 mM Tris-HCl at pH 8.0 or thereabouts, 2% SDS, and from 100-500μg/ml proteinase K.

The above refers to embodiments of the invention where fixed cells of asample are be treated with proteinase K to prepare a cell lysate fromwhich proteinaceous material is removed before further preparativeactions on the nucleic acid material. A non-limiting example of aproteinaceous material removal step beyond the use of phenol or GITCdescribed above is the use of an aqueous solution of anionic,polyelectolyte material that bind proteinaceous material and/or divalentcations. Such material may be particulate in nature and/or applied as aslurry, such as available from Ambion. Following removal of theproteinaceous material, the sample is optionally DNased and then usedfor RNA amplification. If the optional DNase is used, a proteinaceousmaterial removal and/or denaturation step can be used before the stepsfor RNA amplification.

Generation and Use of Gene Expression Level Data

Data of the gene expression level data from an FF or FFPE sampleobtained by the practice of the methods of the present invention arepreferably organized into one or more data fields of a computer readablemedium comprising a plurality of data fields. Preferably, the data is inthe form of expression values or indices that may be correlated withother data from the sample donor. The data fields may be optionallyorganized as one or more datasets and/or one or more data structures. Adata field is stored in a range of addresses in said computer readablemedium and may be treated as representing gene expression level datafrom an FFPE sample.

Generation of gene expression data is preferably by use of hybridizationto an array, such as a microarray as described herein. Nucleic acidprobes containing various gene sequences are individually located atdefined positions of a microarray. The probes are preferably immobilizedon the microarray and represent different genes or gene fragments,optionally having a commonality. Non-limiting examples of commonalitiesinclude expectation that they may be expressed in a given cell type,tissue, or organ; expression in a disease state or unwanted condition;similar biological function(s); or are all the expressed genes for agiven organism. Alternatively the invention may be practiced with theuse of materials that are capable of being sorted into an array, such asthat available from Illumina.

Various technologies are known for the manufacture of microarrays, andthey may be composed of probes located at a variety of densities.Non-limiting examples include from about 10 to about 500,000 probes (andthus gene sequences) in a square centimeter. The probes of suchmicroarrays are hybridized to labeled nucleic acid molecules derivedfrom an FF or FFPE sample as described herein. The observed intensitiesof the hybridization to individual probes reflect expression levels ordata of individual sequences in the FF or FFPE sample.

There are generally control samples, derived from mRNA of a known sourceand/or quantity, and test samples, derived from mRNA from an FF or FFPEsample as described herein. One non-limiting example of a control sampleare normal cells, preferably from the same FF or FFPE sample used forthe test sample, which would contain non-normal cells. Normal andnon-normal cells can be isolated by use of microdissection as describedherein and generally used in the art.

The control and/or test sample is used in combination with a referencemRNA, such as that which acts as a control between microarrayexperiments, with one or more non-zero signals for expression of varioussequences. Non-limiting examples include the human, rat, and mouseUniversal Reference RNA from Stratagene. The test samples may be thatfrom an FF or FFPE sample of a subject suffering from a disease or whichhas been treated with a drug or other agent. The samples may also bethose from tumors that respond to a particular treatment or drug regimenand those that do not respond. Gene expression levels in suchdifferential samples may also be evaluated against each other andagainst control(s) to identify gene expression levels that arecorrelated with one sample and not the other.

Preferably, the hybridization of various samples is conducted under thesame conditions, and in particularly preferred embodiments, the controland test samples are labeled differently and hybridized to the samemicroarray. Preferred labels are fluorescent, such as, but not limitedto red and green (e.g. Cy5 and Cy3) mono-reactive dyes from Amersham,used to directly or indirectly label nucleic acid molecules. The datafrom each hybridization, whether as raw hybridization signal intensitiesor after manipulations such as, but not limited to, spot filtering,background correction, and/or normalization, may be stored in a computerreadable medium as described herein. Preferably, the data is stored asnormalized ratios of test sample intensities to control sample(reference RNA) intensities although other forms of processed data,include that which adjusts for statistical variables in the samples andraw expression level data, to produce an expression value or index mayalso be used. The data is preferably loaded into data fields tofacilitate the analysis of the results in comparison to otherinformation concerning the subject from which the FFPE sample wasobtained. Other data, such as that on each sample, hybridizationconditions, and microarray information, are optionally stored with theabove data.

The hybridization signal intensities are preferably measured by amicroarray reader/analyzer. This is generally conducted with variousknown hardware and software components for use with hybridizationexperiments and the microarray reader/analyzer outputs raw or processedexpression data for each site or element of a microarray. The data mayinclude fluorescence intensity values for each element on themicroarray. The processed data permits a determination of expression ornon-expression of individual gene sequences, optionally as a ratiorelative to a control. Optionally, the level of any expression can bebased on hybridization data from multiple sites having the same ordifferent probes for given gene sequence, such as multiple probes for agiven gene sequence. The processed levels may be averaged before use.

Gene expression data may be stored in the same or a different file withother data, such as, but not limited to, the locations and identities ofgene sequences represented on the microarray, FF or FFPE donorinformation, microarray design information, biological information, datasource, FF or FFPE sample information, descriptions of the experimentalsamples and additional experimental data, and hybridization information.

The information on gene expression, represented as hybridization signalintensities (raw data), or expression indices (such as ratios of rawintensities), are “expression data” and reflects the expression ofvarious gene sequences within an FF or FFPE sample. The expression datamay optionally include a message and/or a series of prompts to promptthe entry of additional information related to the expression data, theFF or FFPE sample from which the data was obtained, or the subject fromwhich the sample was obtained. Non-limiting examples include outcomedata from the subject from which the sample was obtained, such asdiagnosis, prognosis, treatment, response to treatment, and/or actualoutcome(s) experienced by the subject over time. The expression data andthe prompts may be in the form of data fields stored in a range ofaddresses of a computer readable medium.

A computer readable medium comprising the expression data may optionallyfurther comprise an “outcome data” object which serves as a central unitof information that contains not only the expression data, but alsoreceives outcome data of the subject(s) from which the FF or FFPEsample, and thus expression data, was obtained. The outcome data mayalso be considered the phenotypic data from the sample donor, whichincludes donor age, demographics, and history; disease history;diagnosis history; treatments applied and responsiveness thereto;mortality; recurrence of disease, including changes in the form of thedisease upon recurrence; and other information as described above. Theoutcome data object may be stored in a range of addresses separate fromthe expression data or in a range of addresses that also stores a datafield representing expression data. When the outcome data object iscreated, it has locations set aside to store phenotypic information ofthe outcome(s) experienced by the subject(s). This is a differentapproach from databases that only store outcome information because theoutcome object also contains the expression data. This provides anadvantage not previously available because the outcome object can beused to correlate the expression data with the phenotypicdata/outcome(s) to identify the expression of particular gene sequencesas linked with one or more phenotypic outcome(s). It also permits theobject to be passed from one location or source to another whilecontaining all information relating to one or more outcomes. Thesebenefits permits greater ease and speed of use while minimizing thelikelihood of lost information.

After creation of the outcome data object, it is ready to receivevarious phenotypic and outcome information or data from a user or othersource. In a preferred embodiment, outcome data is introducedelectronically. The expression data of an outcome data object may beupdated at anytime. Such an update will necessarily generate an updatedoutcome data object, optionally capable of receiving outcome data fromthe source corresponding to the source of the updating expression data.Such updated expression data may supersede and replace previousexpression data.

A user may input outcome data into an outcome data object in response toa prompt for outcome information, which may be displayed from theexpression data. The outcome information is stored in a data field ofthe outcome data object adapted to receive and store outcome data, whichmay be textual or numerical in form. The outcome data object alsooptionally permits a user to enter additional information not limited tooutcome information.

After receipt of outcome data, the expression data and outcome data maybe used to correlate the expression of one or more gene sequences asassociated with one or more outcomes. Stated differently, the expressiondata (such as expression indices for various gene sequences) isassociated with phenotypic data to identify various indices and genesequences as correlated with outcome(s). The expression indices may bearranged in a data matrix such as a table showing individual indices forindividual gene sequences of individual FF or FFPE samples. Theidentifiers of the individual samples are then used to associatephenotypic data from the donors of the samples with the expressionindices. This association process may also be described as constructinga model or expression profile to explain correlations between expressionindices and phenotypic data for individual samples. Two general modelingmethods that may be used in this aspect of the invention are statisticalmodels and those based upon artificial intelligence. Non-limitingexamples of the former include logistic regression and classificationtrees. These may be used to predict whether a particular expressionindex is predictive of a phenotypic outcome. A non-limiting example ofthe latter is a neural network.

Model building may be viewed as supervised learning based upon theexpression indices and phenotypic data, which may be used as a trainingset upon which a model or profile is constructed. The resultant model orprofile is preferably built to minimize error rates, such as byincreasing the confidence/probability/likelihood level at which anexpression index would be identified as predictive. This may also bereferred to optimization of the model or profile, which may also resultin the reduction in the actual number of expression indices included aspredictive of an outcome. The invention provides for the ability toconstruct multiple models or profiles from the same expression data andphenotypic data, all of which may be optimized before being compared andsubject to selection for possible use.

Model construction and selection are preferably conducted with theapplication of domain knowledge to include or exclude data based uponrecognition of their relevance or importance to the model or profilebeing sought. As a non-limiting example, the recognition that genesequence “A” express a protein product “A prime” which in turn controlsexpression of expression of gene sequence “B” is relevant to modelconstruction to potentially adjust the model to account treat increasesor decreases of “B” expression as corresponding to similar increases ordecreases in “A” expression rather than as an independent index that canbe correlated to phenotypic data. Domain knowledge also refers to therecognition of the significance of data analysis techniques as preferredfor use in model construction. As a non-limiting example, the use ofPearson's correlation (Pearson Product Moment Correlation) to relategene expression indices with phenotypic data as a linear relationship inmany cases.

A model or profile after selection can be validated by use of additionalexpression data and phenotypic data of an FF or FFPE sample. As anon-limiting example, if a model is constructed and selected wherein adecrease in expression of gene sequence “X” is correlated with patientmortality within 24 months, then the model can be validated based uponits ability to predict the phenotypic outcome of mortality within 24months of a sample donor if the sample has the same decrease in genesequence “X” expression. Once validated, the model or profile may beconsidered predictive for various phenotypic outcome(s) based uponparticular gene expression indices. Of course the model may be refinedor altered by use of a different training set or additional dataintroduced into an existing training set or different selection criteriaor application of different domain knowledge and then re-validated.Models produced by the present invention preferably are those where theexpression level of a single gene sequence, or 2-5 or 5-10 genesequences is predictive of a phenotypic outcome, although the use of10-20, 20-30, 30-40, 40-50 or more than 50 gene sequences may also beused in a model.

In preferred embodiments of the invention, the expression data comprisesgene expression information from multiple FF or FFPE samples fromsubjects with the same disease, unwanted condition, or biologicalstatus. The phenotypic or outcome data is preferably information on oneor more outcomes from the donor of the FF or FFPE samples used toproduce the expression data.

By way of example offered to improve the understanding of the inventionand not intended to limit the scope of the invention, an outcome to becorrelated with expression data may be responsiveness of a cancer to aparticular treatment regimen, such as breast cancer to tamoxifen. Theoutcome may be disease status (afflicted or disease free) at varioustimes after start of tamoxifen treatment. This outcome data may be usedto correlate one or more gene sequences the (increased or decreased)expression levels of which is associated with either success or failureof tamoxifen treatment at various times after start of treatment. Thecorrelation may also be used to identify one or more gene sequences the(increased or decreased) expression levels of which defines a populationof subjects having such expression levels and as benefiting or notbenefiting from treatment with tamoxifen. The populations may also beviewed as those with breast cancer that is sensitive or resistant totamoxifen.

The correlation may also be used to identify subpopulations such assubjects with gene sequence levels which are associated with long termor short term success with tamoxifen treatment. These subpopulations mayalso be viewed as those subjects with various expected (or projected)survival times.

Another non-limiting example is the use of training data set from FFPEspecimens (excision biopsies) from women >50 yrs. old who are ER(+),node (−), and tumors less than 2 cm (at the greatest dimension).Preferably, at least 10 samples from women of each group are used; morepreferred is the use of at least 15, at least 20, at least 25, or atleast 50 samples from each group. The women will have undergone surgeryand been given tamoxifen for five years. A subset of these women willhave had recurrence of disease and a subset will not. Model building(gene expression profiling) on the subset of women whose diseaserecurred in comparison to those without recurrence permits theidentification of gene sequence(s) the expression of which arepredictive of breast cancer recurrence or non-recurrence in such apatient population. The patients in whom recurrence occurred or did notoccur are subpopulations as provided by the instant invention.

As would be obvious to the skilled practitioner, the above examples areexemplary in nature and the responsiveness to other drugs or treatmentregimens, including but not limited to radiation therapy or combinationradiation and chemotherapy, may be the focus in applications of theinstant invention. Additionally, this aspect of the invention is notlimited to analyses with therapeutic outcomes. For example, correlationswith life expectancies or the occurrence of metastases may also bepracticed by use of the instant invention.

The outcome data object thus provides a single contained unit ofinformation for the analysis and comparison of expression data andoutcome data. An analogy to the object is a folder or file where allinformation for a correlation of outcome to expression can be placed.The file can then be carried from one individual or location to anotherfor analysis of the data therein or the introduction of additionalexpression and/or outcome data. Because expression level data isgenerated from unselected polyadenylated mRNA levels in FF or FFPEsamples as provided by the present invention, the expression data ismore complete and thus permits more comprehensive identification of genesequence expression level(s) as correlated with outcome(s).

Using an outcome data object also opens up a wide variety of options. Asnoted above, the object can be used to correlate gene expression levelsand one or more outcomes to define a gene “expression profile”comprising gene expression levels that are associated with saidoutcome(s). The “expression profile data” represents the range ofexpression level(s), optionally in the form of hybridization signalintensities or ratios thereof or other expression indices, that areassociated with an outcome. The expression profile data may optionallyinclude a message and/or a series of prompts to prompt the entry ofadditional information, such as the expression levels of a sample forcomparison to the expression profile, which would be used as apredictive model. The expression profile data and the prompts may be inthe form of data fields stored in a range of addresses of a computerreadable medium. This medium may be the same or different from thatcomprising a expression data and an outcome data object.

The present invention also provides a computer readable mediumcomprising the expression profile data, which may optionally furthercomprise a “profile data” object. The profile data object serves as acentral unit of information that contains not only the expressionprofile data, but also receives expression data from a test sample. Thetest sample may be an FFPE sample with a known outcome to test theability of the expression profile data to identify the outcome forvalidation purposes. Alternatively, the test sample may be a fresh,frozen, or recent FF or FFPE tissue sample from a subject afflicted witha disease or seeking treatment to predict the subject's outcome, orprovide information on the efficacy of various treatments, by comparisonto the expression profile data.

As a non-limiting example, the present invention provides a means toidentify gene expression profiles associated with various stages ofbreast cancer, such as atypical ductal hyperplasia (ADH), ductalcarcinoma in situ (DCIS), and invasive ductal carcinoma (IDC). Theexpression profile data associated with each of these stages may be partof a breast cancer profile data object which is able to receiveexpression data from a test sample of a patient who has, or is suspectedof having, breast cancer. A comparison of gene expression level(s) ofthe test sample and the profiles permits the determination that thepatient has none, one, or a combination of the above described stages ofbreast cancer. The expression data on the test sample may generated bythe use of (global) polyadenylated mRNA amplification as describedherein or by the use of PCR based amplification of gene sequences theexpression of which are relevant to the breast cancer expressionprofiles. The use of global mRNA amplification permits the resultingexpression data of a test sample to be compared and analyzed with otherexpression profiles.

The profile data object may be stored in a range of addresses separatefrom the expression profile data or in a range of addresses that alsostores a data field representing expression profile data. When theprofile data object is created, it has locations set aside to storeexpression level data from one or more test samples. The expressionlevel data is preferably received into one or more data fields of theobject that have been adapted for such receipt and for ready comparisonto the expression profile data. This provides the ability to predictoutcomes based on gene expression level(s) and correlation to thearchive of FF and/or FFPE samples and historic outcomes associatedtherewith.

After creation of the profile data object, it is ready to receivevarious expression level information or data from a user or othersource. In a preferred embodiment, expression level data from a testsample is introduced electronically and directly from a microarrayreader. The expression profile data of a profile data object may beupdated at anytime. Such an update will necessarily generate an updatedprofile data object, which may supersede and replace any previousobject. Because the expression profile data is generated from expressionlevel data that reflects unselected polyadenylated mRNA levels asprovided by the present invention, the expression profile data is morecomplete and comprehensive. The invention can thus provide multiple genesequences, the expression levels of which are associated with anoutcome. The invention also allows subsets of an expression profile tobe identified and correlated with an additional outcome.

In an alternative embodiment of the invention, the expression profiledata may be adapted into a spreadsheet program for reviewing the profiledata and optionally for comparison and analysis with expression datafrom a test sample. The program is preferably adapted to be capable ofanalyzing the expression data in comparison to the profile data todetermine the outcome associated with the expression data. Otheranalysis modules (software) may be used or developed to utilize theadapted profile data to associate an outcome with a test sample.

The invention therefore provides a computer readable medium having aplurality of data fields stored on the medium and representing a datastructure, such as expression data or expression profile data,comprising a first data field representing (expression or expressionprofile) data that is to be correlated or analyzed with input (outcomedata or test sample expression data) information, said first data fieldbeing stored in a range of addresses in said computer readable medium;one or more receiver objects that will receive said input information,each receiver object being stored in a separate range of addresses insaid computer readable medium, wherein each receiver object comprises adata field adapted for storing input information for correlation oranalysis with said first data field.

In an alternative embodiment, the first data field is stored in a rangeof addresses used by one of the receiver objects. Moreover, the computerreadable medium may optionally comprising a prompt field adapted forstoring one or more data prompts to elicit entry of input information,which may be outcome information from a human patient from which an FFPEsample was obtained and used for generation of said expression data.

A preferred embodiment of the invention is a computer readable mediumcontaining a gene expression profile comprising a plurality of datafields stored on the medium and representing a data structure andcomprising at least one data field representing expression profile datastored in a range of addresses and a profile data receiver object thatwill receive gene expression data for correlation with said expressionprofile data. The receiver object is stored either in a separate rangeof addresses or in addresses that also store said at least one datafield. The medium may optionally comprising a prompt field adapted forstoring one or more data prompts to elicit entry of input information,which may be expression data from cells of a tissue sample from a humanpatient.

The present invention also provides a system and method for generatingexpression data for inclusion in a computer readable medium thatoptionally comprises a receiver object to receive outcome informationfor correlation with said data. The invention further provides a systemand method for correlating said expression data with said outcomeinformation such that expression level(s) of one or more gene sequencesis/are associated or linked with said outcome. Moreover, the inventionprovides a system and method for generating a gene expression profilethat is correlated with an outcome for inclusion in a computer readablemedium. The medium optionally comprises a receiver object to receivetest sample expression data for comparison and analysis with said geneexpression profile. A system and method for said comparison and analysisis also provided. Preferably, the systems and methods of the inventionare computer implemented and optionally stored as computer executableinstructions on a computer readable medium.

As explained further below, the invention provides data structures ordata sets comprising data that is to be used with information receivedby a receiver object. Embodiments of the invention include means forcreating said data structures or data sets as well as said objects.Preferably, the data structures or data sets are created directly orindirectly via the analysis of gene expression as reflected inpolyadenylated mRNA from FF and/or FFPE samples. The creation of geneexpression data is an initial activity block of the invention. Theactivity may include the creation of prompts for input information aswell as the creation of a receiver object to receive such information. Akey feature of the invention is the use of expression data representingpolyadenylated mRNA levels in combination with a receiver object as acentral repository.

After receipt of input information, the next activity block is thecorrelation of said information with the expression level(s) of one ormore gene sequences as found in the expression data. The results of thecorrelation are used as the data for additional data structures or datasets in the next activity block. The data structures or sets comprisegene expression profile data that is to be used with informationreceived by one or more additional receiver objects. Means for creatingsaid data structures or sets are also included in embodiments of theinvention and are practiced as another activity of the invention. Theactivity may include the creation of prompts for input information aswell as the creation of said receiver object(s) to receive suchinformation. A key feature of the invention is the ability to use theexpression profile data and input expression data from a test sample topredict the outcome of the subject from which the sample was obtained.The prediction is based upon the expression data (polyadenylated mRNAlevels) from the FF and/or FFPE samples correlated with subjectoutcome(s) post sampling.

The prompts or a sequence of prompts that will be displayed to a usermay be any that are appropriate to direct the entry of the requestedinformation. Non-limiting examples related to outcome informationinclude prompts for a disease or condition, as well as conditions thatmay be a subtype or stage thereof; treatment protocol(s) used; outcomeof treatment(s); progress of the disease over time; survival time postsampling (based upon a relevant cause of death); and subsequent disease(e.g. metastatic cancer following a primary cancer). Non-limitingexamples related to test sample expression data information includeprompts for expression data (raw, processed or normalized); themicroarray and probe sequences used; a suspected disease or condition;and type and/or age of sample. In one embodiment, the prompts are textfields that are displayed to the user. Generally, the informationrequested by the prompt is practically limited only by relevance to thetask of expression profiling as disclosed herein. A variety ofinformation can thus be requested by the prompts.

As described herein, receiver objects allows information received forcorrelation and analysis relative to expression data or expressionprofile data to be stored as part of the object. Thus, receiver objectscontain data fields needed to store any appropriate informationreceived. The receiver object may alternatively be part of an analysisobject which is adapted to conduct correlation, analysis, and/or othercomparison functions as described herein. Alternatively, and if ananalysis module is to be used, the receiver objects may containinformation that allows such an analysis module to extract relevantinformation and analyze or display such information for analysis by auser. Analysis is preferably conducted by any type of analysis moduleadapted for analyzing or comparing information received to expressiondata or expression analysis data.

In one embodiment, the analysis module is an adapted spreadsheet programwhich allows correlation, analysis and/or other comparison of thereceived information with said data. As a non-limiting example, the datamay comprise a plurality of prompts that identify specific informationitems requested for use with the data Each prompt may represent a row ina spreadsheet program and each information item received from the usermay be placed in a column of the spreadsheet. A row may represent aparticular outcome, such as sensitivity of a disease to a particulardrug treatment, while the columns represent this outcome information foreach FFPE sample used to generate the expression data to be used. Theanalysis module in this case would be adapted to correlate the outcomeinformation with the expression level(s) of one or more gene sequencesto construct a model as described herein.

Because the information received by the receiver object(s) must becommunicated to the object(s), some embodiments of the inventioncomprise means for the communication of the information by electronicmeans. This may be conducted by a communications processor that isoptionally directly linked to electronic devices (such as but notlimited to databases containing outcome information or a microarrayreader/analyzer/image processor) that contain the information to becommunicated.

In another embodiment of the invention, an FF or FFPE expressioninformation processing system is provided. The system is preferablycomputer implemented and comprises data fields and structures andoptionally objects as described herein. The system preferably alsocomprises instructions for methods or procedures that processesexpression data obtained from a microarray hybridization and stores itinto a computer readable medium as described herein.

A further embodiment of the invention is a computer readable mediumcomprising instructions for a computer to store expression data, such asthat from a microarray hybridization. The instructions preferablycomprise generating the expression data from expression signalintensities from at least one microarray and storing at least one dataset or structure containing the data. The instructions optionallyinclude storing the instructions as well; storing the raw or processedor normalized data; or summarizing the expression data using asummarization method.

The invention also provides a system to store expression data orexpression profile data comprising means for generating said data fromhybridization signal intensities from one or more microarrays and/ormeans for storing said generated data.

Preferred expression data for the practice of the invention is derivedfrom FFPE samples from subjects afflicted with a disease or unwantedcondition wherein cells of a subject have aberrant or altered geneexpression (including responses to infection such as by bacteria,mycobacteria and fungi). Non-limiting examples include cancer, viralinfection, autoimmune diseases, arthritis, diabetes and other metabolicdiseases.

Definitions of Terms Used Herein

A “sequence” or “gene sequence” as used herein is a nucleic acidmolecule or polynucleotide composed of a discrete order of nucleotidebases. The term includes the ordering of bases that encodes a discreteproduct (i.e. “coding region”), whether RNA or proteinaceous in nature,as well as the ordered bases that precede or follow a “coding region”.Non-limiting examples of the latter include 5′ and 3′ untranslatedregions of a gene. It is appreciated that more than one polynucleotidemay be capable of encoding a discrete product. It is also appreciatedthat alleles and polymorphisms of the disclosed sequences may exist andmay be used in the practice of the invention to identify the expressionlevel(s) of the disclosed sequences or the allele or polymorphism.Identification of an allele or polymorphism depends in part uponchromosomal location and ability to recombine during mitosis.

The terms “correlate” or “correlation” or equivalents thereof refer toan association between expression of one or more sequences and aphysiologic state of a cell to the exclusion of one or more other statesby use of the methods as described herein. The invention provides forthe correlation between changes in gene sequence expression levels andoutcomes and treatments encountered by subjects from whom an FFPE samplewas obtained. Increases and decreases may be readily expressed in theform of a ratio between expression in a non-normal cell and a normalcell such that a ratio of one (1) indicates no difference while ratiosof two (2) and one-half indicate twice as much, and half as much,expression in the non-normal cell versus the normal cell, respectively.The normal and non-normal cells are preferably from the same FFPEsample. Expression levels can be readily determined by quantitativemethods as described below.

A “polynucleotide” is a polymeric form of nucleotides of any length,either ribonucleotides or deoxyribonucleotides linked by phosphodiesterbonds and encompasses the strand of a given sequence as disclosed hereinas well as the complementary strand of a given sequence. The term refersonly to the primary structure of the molecule. Thus, this term includesdouble- and single-stranded DNA and RNA as well as analogs thereofcomprising a non-phosphodiester backbone. It also includes known typesof modifications including labels known in the art, methylation, “caps”,substitution of one or more of the naturally occurring nucleotides withan analog, and internucleotide modifications such as uncharged linkages(e.g., phosphorothioates, phosphorodithioates, etc.), as well asunmodified forms of the polynucleotide.

The term “amplify” is used in the broad sense to mean creating anamplification product can be made enzymatically with DNA or RNApolymerases. “Amplification,” as used herein, generally refers to theprocess of producing multiple copies of a desired sequence, particularlythose of a sample. “Amplification” may also be used in the context ofDNA amplification wherein copies of coding sequences within the cellulargenome are increased. “Multiple copies” mean at least 2 copies. A “copy”does not necessarily mean perfect sequence complementarity or identityto the template sequence. Methods for amplifying mRNA are generallyknown in the art, and include reverse transcription PCR (RT-PCR) andthose described herein.

By corresponding is meant that a nucleic acid molecule shares asubstantial amount of sequence identity with another nucleic acidmolecule. Substantial amount means at least 95%, usually at least 98%and more usually at least 99%, and sequence identity is determined usingthe BLAST algorithm, as described in Altschul et al. (1990), J. Mol.Biol. 215:403-410 (using the published default setting, i.e. parametersw=4, t=17). Alternatively, RNA may be directly labeled as thecorresponding cDNA by methods known in the art.

A “microarray” is a linear or two-dimensional array of preferablydiscrete regions, each having a defined area, formed on the surface of asolid support such as, but not limited to, glass, plastic, or syntheticmembrane. The density of the discrete regions on a microarray isdetermined by the total numbers of immobilized polynucleotides to bedetected on the surface of a single solid phase support, preferably atleast about 50/cm², more preferably at least about 100/cm², even morepreferably at least about 500/cm² or at least about 1,000/cm². In someembodiments, the arrays contain less than about 500, about 1000, about1500, about 2000, about 2500, or about 3000 immobilized polynucleotidesin total. As used herein, a DNA microarray is an array ofoligonucleotides or polynucleotides placed on a chip or other surfacesused to hybridize to amplified or cloned polynucleotides from a sample.Since the position of each particular group of probes in the array isknown, the identities of a sample polynucleotides can be determinedbased on their binding to a particular position in the microarray.

Because the invention relies upon the identification of sequences thatare over- or under-expressed, one embodiment of the invention involvesdetermining expression by hybridization of mRNA, or an amplified orcloned version thereof, of a sample to a polynucleotide of a disclosedsequence. Preferred polynucleotides of this type contain at least about20, at least about 22, at least about 24, at least about 26, at leastabout 28, at least about 30, at least about 32, at least about 34, atleast about 36, at least about 38, at least about 40, at least about 42,at least about 44, or at least about 46 consecutive bases of a sequencethat is not found in other human sequences. The term “about” as used inthe previous sentence refers to an increase or decrease of 1 from thestated numerical value. Longer polynucleotides may of course containminor mismatches (e.g. via the presence of mutations) which do notaffect hybridization to the nucleic acids of a sample. Suchpolynucleotides may be label to assist in their detection;alternatively, the nucleic acids to which such polynucleotides willhybridize may be labeled. Such polynucleotides may also be immobilized,such as by attachment to a solid support.

Even more preferred are polynucleotides of at least or about 50, atleast or about 100, at least about or 150, at least or about 200, atleast or about 250, at least or about 300, at least or about 350, atleast or about 400, at least or about 450, or at least or about 500consecutive bases of a sequence that is not found in other sequences inthe human genome. The term “about” as used in the preceding sentencerefers to an increase or decrease of 10% from the stated numericalvalue. Preferably, the sequences are found in the 3′ portion immediatelyupstream of the polyA tail of an expressed mRNA. The polynucleotides mayof course contain minor mismatches which do not affect hybridization tothe nucleic acids of a sample.

In another embodiment of the invention, all or part of a disclosedsequence may be amplified and detected by methods such as the polymerasechain reaction (PCR) and variations thereof, such as, but not limitedto, quantitative PCR (QPCR), reverse transcription PCR (RT-PCR), andreal-time PCR, optionally real-time RT-PCR. Such methods would utilizeone or two primers that are complementary to portions of a disclosedsequence, where the primers are used to prime nucleic acid synthesis.The newly synthesized nucleic acids are optionally labeled and may bedetected directly or by hybridization to a polynucleotide of theinvention. The newly synthesized nucleic acids may be contacted withpolynucleotides (containing sequences) of the invention under conditionswhich allow for their hybridization.

The term “label” refers to a composition capable of producing adetectable signal indicative of the presence of the labeled molecule.Suitable labels include radioisotopes, nucleotide chromophores, enzymes,substrates, fluorescent molecules, chemiluminescent moieties, magneticparticles, bioluminescent moieties, and the like. As such, a label is acomposition detectable by spectroscopic, photochemical, biochemical,immunochemical, electrical, optical or chemical means.

“Expression” and “gene expression” refers to transcription of nucleicacid material, such as the sequences of the invention, as well as thepossibility that the transcribed sequences may be translated. The“level” of (gene) expression refers to the amount of expression, whichmay be increased or decreased relative to a control or normal level ofexpression. While increases and decreases may be readily determined byrelative levels of mRNA production, decreases may also be determined bypromoter status (such as methylation or other types of inactivation) ofthe sequences found to exhibit decreased expression.

As used herein, the term “comprising” and its cognates arc used in theirinclusive sense; that is, equivalent to the term “including” and itscorresponding cognates.

Conditions that “allow” an event to occur or conditions that are“suitable” for an event to occur, such as hybridization, strandextension, and the like, or “suitable” conditions are conditions that donot prevent such events from occurring. Thus, these conditions permit,enhance, facilitate, and/or are conducive to the event. Such conditions,known in the art and described herein, depend upon, for example, thenature of the nucleotide sequence, temperature, and buffer conditions.These conditions also depend on what event is desired, such ashybridization, cleavage, strand extension or transcription.

Sequence “mutation,” as used herein, refers to any sequence alterationin the sequence of a gene disclosed herein interest in comparison to areference sequence. A sequence mutation includes single nucleotidechanges, or alterations of more than one nucleotide in a sequence, dueto mechanisms such as substitution, deletion or insertion. Singlenucleotide polymorphism (SNP) is also a sequence mutation as usedherein. Because the present invention is based on increases anddecreases in sequence expression, mutations in coding and non-codingregions of genes may also be assayed in the practice of the invention.

“Detection” or “detect” includes any means of detecting, includingdirect and indirect detection of gene expression and changes therein.For example, “detectably less” expression may be observed directly orindirectly, and the term indicates any reduction (including the absenceof detectable signal). Similarly, “detectably more” product means anyincrease, whether observed directly or indirectly.

Oligo or poly dT sequences or primers refers to the presence of at leastabout 8 consecutive dT bases in a polynucleotide. Preferably, there arefrom about 8 to about 20, about 21 or about 30 consecutive dT bases.More than about 30 consecutive dT bases may also be used.

Random primers refers to the use of at least about 6 consecutive basesof random sequence as a primer for the synthesis of a nucleic acidstrand. Preferably, the primers are of 6, 7, 8, 9, or 10 consecutivebases. As will be appreciated by the skilled person, primers that aretoo short will not be able to stably hybridize to a template strand toprime polynucleotide polymerization. Primers that are too long may notdiffuse sufficiently fast to prime synthesis from a sufficient number ofcomplementary sequences.

“Disease” refers to a change in the normal status of a living organismor a tissue or organ thereof that impairs the performance of theorganism's physiological functions. A disease may be a result ofexposure to environmental factors (such as, but not limited to, chemicalagents or radiation), to an infective agent (such as, but not limitedto, bacteria, viruses, or parasites), to congenital defects of theorganism (such as, but not limited to, genetic mutations which maymanifest in combination with environmental factors or at different timesin the life of the organism). A disease may also be due to a combinationof the above as well as descriptive of a set of related diseases. Anon-limiting example of the latter is the use of the term “breastcancer” to refer to a group of cancer diseases in breast tissue as wellas a group of subtypes of breast cancer.

Unless defined otherwise all technical and scientific terms used hereinhave the same meaning as commonly understood to one of ordinary skill inthe art to which this invention belongs. The practice of the presentinvention will employ, unless otherwise indicated, conventionaltechniques of molecular biology (including recombinant techniques),microbiology, cell biology, biochemistry, and immunology, which arewithin the skill of the art. Such techniques are explained fully in theliterature, such as, “Molecular Cloning: A Laboratory Manual”, secondedition (Sambrook et al., 1989); “Oligonucleotide Synthesis” (M. J.Gait, ed., 1984); “Animal Cell Culture” (R. I. Freshney, ed., 1987);“Methods in Enzymology” (Academic Press, Inc.); “Current Protocols inMolecular Biology” (F. M. Ausubel et al., eds., 1987, and periodicupdates); “PCR: The Polymerase Chain Reaction”, (Mullis et al., eds.,1994). Primers, oligonucleotides and polynucleotides employed in thepresent invention can be generated using standard techniques known inthe art.

Having now generally described the invention, the same will be morereadily understood through reference to the following examples which areprovided by way of illustration, and are not intended to be limiting ofthe present invention, unless specified.

EXAMPLE 1 Selected Materials and Methods

Proteinase K digestion before extracting RNA:

5-10 μm thick formalin-fixed paraffin embedded (FFPE) tissue sectionsmounted on frosted slides underwent deparaffinization, H & E stainingand dehydration. Tissue lysates prepared from whole sections or lasercaptured cells of approximately 3000 to 5000 cells procured using thePixCell II system (Arcturus, Mountain View, Calif.) were treated with asolution comprised of 10 mM Tris pH 8.0, RNA-grade Proteinase K (100 or500 μg/ml, Invitrogen, Carlsbad, Calif.), 2% SDS (Invitrogen, Carlsbad,Calif.) for at least 16 hours at 42° C.

Reverse Transcription:

To generate cDNA for either quantitative RT PCR analysis alone or forRNA amplification, demodified RNAs obtained from the samples werereverse transcribed using either oligo dT or random primers, in areaction comprised of 50 mM Tris-HCl, 37.5 mM KCl, 1.5 mM MgCl₂, 10 mMDTT, 0.5 mM dNTPs (Pharmacia, Piscataway, N.J.), 40 units RNasin(Promega, Madison, Wis.), 200 units Superscript RT II (Invitrogen,Carlsbad, Calif.).

Brief Exemplar of RNA Amplification:

The mRNA component of each RNA preparation was linearly amplified usinga modified version of the RiboAmp™ RNA amplification kit (Arcturus,Mountain View, Calif.). Briefly, the RNA from each sample was primedwith 20 nanograms of an oligo dT primer containing a T7 promotersequence, reverse transcribed and then converted to double stranded cDNAusing random primers. The cDNA templates were then used in an in vitrotranscription reaction using T7 RNA polymerase to generate amplified RNA(aRNA) in the antisense orientation (with sequences complementary tothose of the mRNA used as a template for cDNA synthesis). A second roundof amplification was performed to generate more aRNA, which wassubsequently used as template to prepare fluorescently labeled cDNAprobes for hybridization.

Probe Labeling and Microarray Hybridization:

A portion of the amplified RNA from each sample was used in a cDNAlabeling reaction using 5-(3-aminoallyl)-2′-deoxyuridine-5′-triphosphate(aminoallyl-dUTP) using the Fair Play Kit (Stratagene, La Jolla,Calif.). Cy3 or Cy5 mono-reactive dye (Amersham, Piscataway, N.J.) wasconjugated onto purified cDNA and further purified using QiaQuick PCRPurification columns (Qiagen, Valencia, Calif.). To make fluorescentlylabeled cDNA, Cy5 dye was used for aRNAs from each test sample and Cy3dye was used for a reference aRNA (Universal Human Reference RNA,Stratagene, La Jolla, Calif.). Equal amounts of purified, Cy5-labeledtest sample cDNA was co-hybridized with Cy3-labeled reference cDNA tomicroarrays containing up to 22,000 features in a 40 μl hybridizationsolution (5×SSC, 0.1 μg/μl COT-1 DNA, 0.2% SDS, 50% Formamide) at aprobe concentration of 25 ng/μl for 17 hours at 42° C. in greater than60% humidity.

Obtaining Expression Data:

After hybridization, microarray slides were washed, scanned andquantitated for hybridization signal intensity. Cy5 and Cy3 fluorescenceintensities, after spot filtering/background correction andnormalization, were expressed as normalized ratios of Cy5/Cy3 torepresent the gene expression levels in the test samples with respect tothe universal reference RNA.

EXAMPLE 2 RNA Stability in FFPE Samples and Amplification Thereof

5 μm tissue sections were formalin fixed for 1, 4 or 8 days and thenparaffin embedded. The sections were deparaffinized, rehydrated withgraded ethanols and then treated with Proteinase K at 500 μg/ml at 42°C. for 4 hours in 10 mM Tris-HCl pH 8.0; 2% SDS.

A frozen tissue sample was similarly digested with proteinase K forcomparison.

FIG. 1 shows the results of RNA gel electrophoresis which shows that RNAfrom formalin fixed tissues remains intact in tissues fixed in formalinfor 1 to 8 days. The samples were run in duplicate. “M” denotes an RNAmarker lane.

FIG. 2A shows the results of RNA amplification of the tissue samplesfixed for 1, 4, or 8 days as well as fresh frozen tissue. The sampleswere proteinase K digested, followed by extraction using a GITCcontaining solution and purification on a silica column. The RNA wasamplified as described above. Lanes 1-7 contain an RNA marker, 1 dayFFPE, 1 day FFPE, 4 days FFPE, 8 days FFPE, 8 days FFPE, and 0hour/fresh frozen, respectively.

FIG. 2B shows the results of RNA amplification of tissue samples fixedfor 4 days and analyzed in six lanes. The first lane contains RNAmarkers.

EXAMPLE 3 RNA Amplification from Archival Breast Cancer FFPE Samples

Archival FFPE breast core biopsies of about 1 to 2 years old weretreated as described above in Example 2. The following Table 1summarizes the samples and the yield of amplified RNA therefrom. Theresults are shown in FIG. 3A, where M indicates RNA markers.

TABLE 1 Lane Year Yield aRNA (μg) 1 2002 70.4 (did not work) 2 2002 90.23 2002 98.4 4 2002 110.0 5 2002 93.7 6 2001 100.0 7 2001 90.2 8 200285.5 9 2002 87.9 10 2002 117.0

FIG. 3B shows the results of RNA amplification from four six year oldarchival FFPE breast core biopsies. The samples were analyzed induplicate. The following Table 2 summarizes the samples and the yield ofamplified RNA therefrom. “DCIS” refers to ductal carcinoma in situ;“IDC” refers to invasive ductal carcinoma.

TABLE 2 Sample Cellularity Yield aRNA (μg) 1 30% DCIS 106 2 Same 88 320% DCIS 90 4 Same 131 5 40% IDC 105 6 Same 121 7 50% DCIS 117 8 same127

EXAMPLE 4 RNA Amplification from Archival Bladder Cancer FFPE Samples

Archival FFPE human bladder samples of about 1 to 4 years old weretreated as described above in Example 2. The following Table 3summarizes the samples and the yield of amplified RNA therefrom. T1, Ta,HG, LG, and CIS, refer to superficially invasive, in situ papillary,high grade, low grade, and flat carcinoma in situ, respectively.

The results are shown in FIG. 4, where M indicates RNA markers. Lanes 1,4, and 15 show the results of sub-optimal amplification.

TABLE 3 Lane Most advanced lesion Block age at analysis (days) YieldaRNA (μg) 1 T1 1650 74.64 2 Ta (LG) 1639 102.62 3 Ta (HG) 1602 93.79 4T1 1582 68.88 5 Ta (HG) 1181 112.13 6 T1 1126 85.73 7 Ta (HG) 921 110.38 CIS 921 99.98 9 T1 892 89.42 10 Ta (HG) 738 91.25 11 CIS 541 82.42 12CIS 402 87.41 13 T1 345 94.56 14 CIS 147 84.19 15 T1 133 80.3 16 T1 11278.91

EXAMPLE 5 Consistency of Gene Expression in FFPE Samples

FFPE sample from a patient were used for two independent laser capturemicrodissection (LCM) followed by separate mRNA amplification asdescribed in Example 2. The amplified RNA were used to generate labeledcDNA for hybridization of a microarray comprising 17296 oligonucleotidegene sequence probes. A scatter-plot of the (log) hybridization signalintensities for each probe from the two independent experiments areshown in FIG. 5. Only 148 genes (0.8% of total) showed over a 2-foldvariation between the duplicate hybridizations. The overall correlationcoefficient was 0.96.

EXAMPLE 6 Comparison of Gene Expression in FFPE and Frozen Samples

FFPE and frozen samples from the same patient biopsy were sectioned andused for mRNA amplification as described in Example 2 without lasercapture microdissection. The amplified RNA were used to generate labeledcDNA for hybridization of a microarray. A scatter-plot of the (log)hybridization signal intensities for each probe sequence of themicroarray from the FFPE and frozen samples are shown in FIG. 6. Theoverall correlation coefficient was 0.912.

Similar experiments with RNA amplified from paraffin embedded sectionsthat have been fixed in formalin for 1, 4, or 8 days showed similarreproducibility of gene expression patterns. Correlations of intensitiesbetween such samples are shown in Table 4.

TABLE 4 1 day in formalin 4 days in formalin 4 days in formalin r =0.9212 8 days in formalin r = 0.9328 r = 0.9384

EXAMPLE 7 Demodification of RNA in FFPE Samples

FFPE samples that were fixed in formalin for 4 or 8 days beforeembedding in paraffin were used for RNA extraction followed bydemodification at 70° C. for various times. The samples were thenamplified by RT-PCR using primers positioned to amplify about 110 basesupstream from the polyA site of the beta actin mRNA. The relative yieldof the amplification is shown in FIG. 7, where demodification times of3-8 hours gave good yields.

The samples were also amplified by RT-PCR using primers positioned toamplify about 1000 bases upstream from the polyA site of the beta actinmRNA. The relative yield of the amplification is shown in FIG. 8, wheredemodification times of 3-8 hours gave good yields.

Similar results were observed with FFPE samples that were fixed informalin for 1 day before embedding.

EXAMPLE 8 Comparison of RNA Amplification Techniques

RNA from tissue fixed in formalin for 24 hours and subsequently paraffinembedded was used to prepare total RNA for amplification as described inExample 2. Total RNA was converted to double stranded cDNA (in a firstround) using an oligo dT-T7 primer via use of exogenously suppliedrandom primers to produce the second cDNA strand or by use of“endogenous priming” to produce the second cDNA strand without randomprimers. The product cDNA were used for (“first round”) in vitrotranscription (IVT) to produce amplified RNA that was used to producecDNA in a second round using the same methods as the first round. Theresultant cDNA was used for second round IVT, where biotin wasincorporated into the amplified RNA product to generate aRNA probes forprobe targets on a microarray.

Prior to hybridization, 10-20 μg of biotinylated aRNA was fragmented ina buffer comprised of 20 mM Tris-acetate, pH 8.1, 50 mM KOAc, 15 mMMgOAc which was heated to 95° C. for 35 minutes and then chilled. Thefragmented aRNA was subsequently purified and hybridized to microarraysat a concentration of 0.05 μg/μl, in a buffer comprised of 100 mM MES,1M [Na+], 20 mM EDTA, 0.01% Tween-20, 0.1 mg/ml herring sperm DNA, 0.5mg/ml acetylated BSA for 16 hours at 45° C. The resultant scatter graphshowing the signal intensities at the microarray probe positions isshown in FIG. 9. The X axis is without the use of random primers and theY axis is with the use of random primers. The correlation coefficient ris 0.9173787, indicating that both methods are able to amplify RNA froman FFPE sample for use in the present invention.

REFERENCES

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4. Karsten et al., An evaluation of tyramide signal amplification andarchived fixed and frozen tissue in microarray gene expression analysis.Nucleic Acid Research, 30, E4, 2002.

5. Lewis et al., Unlocking the archive-gene expression inparaffin-embedded tissue. J. Pathology, 195, 66-71, 2001.

6. Lehmann et al. Real-time PCR analysis of DNA and RNA extracted fromformalin-fixed and paraffin-embedded biopsies. Methods, 25, 409-418,2001.

7. Feldman, Reaction of formaldehyde with nucleotides and ribonucleicacid, Biochimica Et Biophysica Acta, 149, 20-34, 1967

8. Specht et al., Quantitative gene expression analysis inmicrodissected archival formalin-fixed and paraffin-embedded tumortissue. American J. Pathology, 158, 419-429, 2001.

9. Cohen et al., Laser microdissection and gene expression analysis onformaldehyde-fixed archival tissue. Kidney International, 61, 125-132,2002.

10. Masuda et al., Analysis of chemical modification of RNA fromformalin-fixed samples and optimization of molecular biologyapplications for such samples. Nucleic Acids Research, 27, 4436-4443,1999.

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All references cited herein are hereby incorporated by reference intheir entireties, whether previously specifically incorporated or not.As used herein, the terms “a”, “an”, and “any” are each intended toinclude both the singular and plural forms.

Having now fully described this invention, it will be appreciated bythose skilled in the art that the same can be performed within a widerange of equivalent parameters, concentrations, and conditions withoutdeparting from the spirit and scope of the invention and without undueexperimentation. While this invention has been described in connectionwith specific embodiments thereof, it will be understood that it iscapable of further modifications. This application is intended to coverany variations, uses, or adaptations of the invention following, ingeneral, the principles of the invention and including such departuresfrom the present disclosure as come within known or customary practicewithin the art to which the invention pertains and as may be applied tothe essential features hereinbefore set forth.

1. A method for amplification and analysis of expressed RNA from cellsof a deparaffinized FFPE (formalin fixed paraffin embedded) sample, saidmethod comprising: synthesizing, with a primer comprising a sequencecomplementary to RNA extracted from said cells of said deparaffinizedFFPE sample, to produce first cDNA strands; amplifying said cDNA strandsto produce amplified molecules; hybridizing said amplified molecules toa microarray; and producing signals from hybridized molecules, whereinthe signals reflect expressed RNA in said cells.
 2. The method of claim1, wherein said RNA is extracted from said cells by a method comprising:obtaining said cells from said sample; digesting said cells withproteinase K to produce digested material; contacting the digestedmaterial with a guanidinium containing compound to produce a mixture;contacting the mixture with a silica matrix to permit RNA binding to thematrix; and eluting the bound RNA after removal of unbound matter. 3.The method of claim 2, further comprising heating said RNA extractedfrom said cells at about 70° C. before contacting said RNA with saidprimer.
 4. The method of claim 1, further comprising synthesizing secondcDNA strands, complementary to said first cDNA strands, by use of randomprimers.
 5. The method of claim 1, wherein said primer is operablylinked to a promoter sequence.
 6. The method of claim 4, wherein saidrandom primers are hexamers, heptamers, octamers, or nonamers.
 7. Amethod of comparing gene expression data to a gene expression profile,said method comprising: obtaining gene expression data by the method ofclaim 1, comparing said data to a gene expression profile generated bygene expression data from one or more FFPE samples from one or moreother subjects, and determining whether said data is the same or similaras said gene expression profile.
 8. The method of claim 1, wherein saidcells are microdissected from said FFPE sample prior to RNA extraction.9. The method of claim 1, wherein said FFPE sample is of a fine needleaspirate (FNA).
 10. The method of claim 1, wherein said FFPE sample isof a core biopsy.
 11. The method of claim 1, wherein said FFPE sample isof a needle biopsy.
 12. The method of claim 1, wherein saiddeparaffinized FFPE sample comprises tumor tissue and the cells of saiddeparaffinized FFPE sample are tumor cells.
 13. The method of claim 12,wherein said tumor tissue is of the pancreas, large intestine, kidney,lung, brain, or a lymphoma.
 14. The method of claim 13, wherein saidtumor tissue is pancreas tissue.
 15. The method of claim 13, whereinsaid tumor tissue is large intestine tissue.
 16. The method of claim 13,wherein said tumor tissue is kidney tissue.
 17. The method of claim 13,wherein said tumor tissue is lung tissue.
 18. The method of claim 13,wherein said tumor tissue is brain tissue.
 19. The method of claim 13,wherein said tumor tissue is of a lymphoma.
 20. The method of claim 12,wherein said expressed RNA is polyadenylated RNA.
 21. (canceled)